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NwV assembly and maturation
by single particle (icosahedral) reconstruction, at 8 A resolution
#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 2, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1608 |
|---|---|
| Title | NwV assembly and maturation |
| Map | Map of NwV VLP capsid |
| Sample | NwV |
| Keywords |  Assembly, maturation |
| Authors | Tang J, Lee KK, Bothner B, Baker TS, Yeager M, Johnson JE |
| Date | Deposition: 2009-03-20, Header release: 2009-04-15, Map release: 2010-11-16, Last update: 2011-08-31 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 2, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Mol. Biol., Vol. 392, Issue 3, Page 803-12, Year 2009 |
|---|---|
| Title | Dynamics and stability in maturation of a T=4 virus. |
| Authors | Jinghua Tang, Kelly K Lee, Brian Bothner, Timothy S Baker, Mark Yeager, John E Johnson Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. |
| Keywords | Amino Acid Sequence, Capsid (chemistry), Cryoelectron Microscopy, Hydrogen-Ion Concentration, Models, Molecular, Molecular Sequence Data, Protein Conformation, RNA Viruses (chemistry), Viral Proteins (chemistry), Virion (chemistry), Virus Assembly |
| Links | PII: S0022-2836(09)00877-8, DOI: 10.1016/j.jmb.2009.07.038, PubMed: 19627990, PMC: PMC2766526 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1608.map ( map file in CCP4 format, 46174 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 452.1 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.74 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Map of NwV VLP capsid | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | NwV |
|---|---|
| Number of Components | 1 |
| Details | Purified |
| Component #1: virus - NwV | |
| Scientific name | Nudaurelia capensis omega virus |
| Common Name | NwV |
| Scientific Name of Species | Nudaurelia capensis omega virus |
| Common Name of Species | NwV |
| NCBI taxonomy | 12541 |
| Empty | No |
| Enveloped | No |
| Isolate | SPECIES |
| Class | VIRUS-LIKE PARTICLE |
| Natural Source | NCBI taxonomy: 7088 Host Species: Lepidoptera Host Category: INVERTEBRATES |
| Shell | Id: 1 , Diameter: 410 A, T Number: 4 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen State | particle |
| Buffer | pH: 5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000, Calibrated: 50000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 500 nm - 5000 nm |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Sampling Size | 7 |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection match |
| Software | Auto3dem |
| CTF Correction | Each image |
| Resolution By Author | 8 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Refinement Space | REAL |
| PDB Entry ID | 1OHF |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1608.xml (6.6 KB) | ||
|---|---|---|---|
| Map data | emd_1608.map.gz (21.2 MB)emd_1608.map_1.gz (11.9 MB)emd_1608.map_2.gz (29.5 MB) | ||
| Images |  emd-1608.gif (113.7 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1608 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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